INDEXDB_RNA(1)

📦 version 2.1, in ubuntu jammy

💖 INDEXDB_RNA 💖

okay so bestie, welcome to indexdb_rna — the little tool from the indexdb family that filters, maps and OTU-picks your NGS reads. section 1 of the manuals, User Commands energy, she's iconic, she's fr fr doing the most 💅

✨ SYNOPSIS ✨

indexdb_rna --ref db.fasta,db.idx [OPTIONS]

like… that's the whole vibe. --ref and you're off 🦋

🌸 DESCRIPTION 🌸

okay so SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. the core algorithm is based on approximate seeds and it's literally built to let you do fast and sensitive analyses of nucleotide sequences. no cap, both at once 🔥

the main application of SortMeRNA is filtering rRNA from metatranscriptomic data. additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). yes she collaborates, she's a team player 🫶

SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. optionally, it can provide high quality local alignments of rRNA reads against the rRNA database ✨

she works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. versatile queen behavior, we love to see it 👑

💜 OPTIONS 💜

🎀 MANDATORY OPTIONS 🎀

  • --ref STRING,STRING — FASTA reference file, index file.

Example:

--ref /path/to/file1.fasta,/path/to/index1

if you're passing multiple reference sequence files, separate them by ':'

Example:

--ref /path/f1.fasta,/path/index1:/path/f2.fasta,path/index2
not optional bestie. --ref is the main character here, she's required, periodt 💅

🦋 OPTIONAL OPTIONS 🦋

  • --fast BOOL — suggested option for aligning ~99% related species (default: off)
  • --sensitive BOOL — suggested option for aligning ~75-98% related species (default: on)
  • --tmpdir STRING — directory where to write temporary files
  • -m INT — the amount of memory (in Mbytes) for building the index (default: 3072)
  • -L INT — seed length (default: 18)
  • --max_pos INT — maximum number of positions to store for each unique L-mer (default: 10000, setting --max_pos 0 will store all positions)
  • -v BOOL — verbose
  • -h BOOL — help
lowkey important: --sensitive is on by default, --fast is off by default. so if you want that 99%-related-species speed run, you gotta say it out loud 😌

that's the whole page, bestie, you ate it 🌈✨

indexdb_rna 2.0 — August 2015 — INDEXDB_RNA(1), mwah, go index something 💖🎀🦋

📦 where this page comes from